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Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis

Overview of attention for article published in Genome Medicine, May 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (76th percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

12 tweeters


13 Dimensions

Readers on

45 Mendeley
2 CiteULike
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Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis
Published in
Genome Medicine, May 2016
DOI 10.1186/s13073-016-0310-3
Pubmed ID

Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Hinrich Gronemeyer


Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. We applied a systems biology approach by combining transcriptome and epigenome data for each step during transformation and integrated transcription factor-target gene associations in order to reconstruct the gene regulatory networks that are at the basis of the transformation process. We identified 142 transcription factors and 24 chromatin remodelers/modifiers (CRMs) which are preferentially associated with specific co-expression pathways that originate from deregulated gene programming during tumorigenesis. These transcription factors are involved in the regulation of divers processes, including cell differentiation, the immune response, and the establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes which are not only co-regulated but also functionally related. Decortication of transcription factor targets enabled us to define potential key regulators of cell transformation which are engaged in RNA metabolism and chromatin remodeling. We reconstructed gene regulatory networks that reveal the alterations occurring during human cellular tumorigenesis. Using these networks we predicted and validated several transcription factors as key players for the establishment of tumorigenic traits of transformed cells. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of the gene regulatory network that is altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 45 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
Unknown 44 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 36%
Researcher 10 22%
Student > Master 3 7%
Other 2 4%
Student > Postgraduate 2 4%
Other 6 13%
Unknown 6 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 19 42%
Agricultural and Biological Sciences 12 27%
Computer Science 4 9%
Nursing and Health Professions 1 2%
Medicine and Dentistry 1 2%
Other 3 7%
Unknown 5 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 02 June 2016.
All research outputs
of 20,464,976 outputs
Outputs from Genome Medicine
of 1,326 outputs
Outputs of similar age
of 278,946 outputs
Outputs of similar age from Genome Medicine
of 8 outputs
Altmetric has tracked 20,464,976 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,326 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.4. This one is in the 41st percentile – i.e., 41% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 278,946 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 76% of its contemporaries.
We're also able to compare this research output to 8 others from the same source and published within six weeks on either side of this one. This one has scored higher than 3 of them.